Re: [galaxy-dev] Unnamed histories proliferating, can't get to my data
Hi Amit, I'm not understanding the original process that results in the problem. You're attempting to upload a file (as an import from an FTP dir), but that file never appears in your current history, or any of your saved histories? --nate On Nov 1, 2012, at 8:48 PM, Karger, Amir wrote: OK, we've made some progress. When we try to do uploads (or, I think, switch histories from the User-Saved Histories page), we get an error from get_history in /www/galaxy.hms.harvard.edu/support/galaxy-dist/lib/galaxy/web/framework/__ init__.py The code that makes it is: # Perhaps a bot is running a tool without having logged in to get a history log.debug( Error: this request returned None from get_history(): %s % self.request.browser_url ) So either self.galaxy_session.current_history is failing to return anything, or get_history is being called without create=False at the wrong time. Does this help narrow down what might be happening? It's not the FTP upload; this issue can happen with uploading through the browser, too. Thanks, -Amir Karger On 10/23/12 2:42 PM, Karger, Amir amir_kar...@hms.harvard.edu wrote: I'm using Galaxy from June, 2012. (Sorry if there's already a fix.) We've got it working in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote current history next to it. But the right pane still shows Unnamed history with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Unnamed histories proliferating, can't get to my data
OK, we've made some progress. When we try to do uploads (or, I think, switch histories from the User-Saved Histories page), we get an error from get_history in /www/galaxy.hms.harvard.edu/support/galaxy-dist/lib/galaxy/web/framework/__ init__.py The code that makes it is: # Perhaps a bot is running a tool without having logged in to get a history log.debug( Error: this request returned None from get_history(): %s % self.request.browser_url ) So either self.galaxy_session.current_history is failing to return anything, or get_history is being called without create=False at the wrong time. Does this help narrow down what might be happening? It's not the FTP upload; this issue can happen with uploading through the browser, too. Thanks, -Amir Karger On 10/23/12 2:42 PM, Karger, Amir amir_kar...@hms.harvard.edu wrote: I'm using Galaxy from June, 2012. (Sorry if there's already a fix.) We've got it working in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote current history next to it. But the right pane still shows Unnamed history with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Unnamed histories
Hi Jelle and Sarah, I can't work on this issue right this moment, but have created an issue to track so it's not forgotten: https://bitbucket.org/galaxy/galaxy-central/issue/767/when-remote_user-true-a-lot-of-new-empty --nate On Jun 3, 2012, at 7:43 AM, Jelle Scholtalbers wrote: Hi Sarah, although I do not have the answer to the issue, I had the same problem when I was using remote_user with apache and ldap authentication. I have too little knowledge of session ids/cookies, and it has been a while (1,5yr), but somehow galaxy thinks you are in a new session and therefor creates a new history. Cheers, Jelle On Fri, Jun 1, 2012 at 11:58 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Dear all, Each time a user connects to our local instance of Galaxy, a new history is automatically created. Therefore, the list of Unnamed history can become very long. Is there a way to reuse the same empty Unnamed history to avoid creating a new one every time? Thank you in advance, Sarah moz-screenshot-5.jpg ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
